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- PDB-4pe5: Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel -

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Basic information

Entry
Database: PDB / ID: 4pe5
TitleCrystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / NMDA receptor / GluN1 / GluN2B / ion channel
Function / homologyIonotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Periplasmic binding protein-like I / Receptor family ligand binding region / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Receptor, ligand binding region / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor ...Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Periplasmic binding protein-like I / Receptor family ligand binding region / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Receptor, ligand binding region / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ligand-gated ion channel / N-methyl D-aspartate receptor 2B3 C-terminus / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / sensitization / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / D2 dopamine receptor binding / NMDA selective glutamate receptor signaling pathway / dendritic branch / positive regulation of Schwann cell migration / response to other organism / extracellularly glutamate-gated ion channel activity / apical dendrite / cellular response to lipid / positive regulation of glutamate secretion / ligand-gated ion channel activity involved in regulation of presynaptic membrane potential / cellular response to dsRNA / glutamate-gated calcium ion channel activity / neurotransmitter binding / calcium ion transmembrane import into cytosol / action potential / interleukin-1 receptor binding / glutamate receptor binding / multicellular organismal response to stress / voltage-gated cation channel activity / glycine binding / parallel fiber to Purkinje cell synapse / response to carbohydrate / NMDA glutamate receptor activity / cellular response to forskolin / glutamate binding / NMDA selective glutamate receptor complex / synaptic membrane / dendrite membrane / response to methylmercury / positive regulation of cysteine-type endopeptidase activity / response to magnesium ion / positive regulation of reactive oxygen species biosynthetic process / response to manganese ion / response to growth hormone / postsynaptic density membrane / response to amine / associative learning / positive regulation of calcium ion transport into cytosol / behavioral fear response / receptor clustering / excitatory synapse / ionotropic glutamate receptor binding / long-term memory / excitatory postsynaptic potential / regulation of MAPK cascade / positive regulation of dendritic spine maintenance / synaptic cleft / positive regulation of excitatory postsynaptic potential / response to cocaine / positive regulation of synaptic transmission / phosphatase binding / response to fungicide / integral component of postsynaptic density membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / response to amphetamine / cellular response to organic cyclic compound / ionotropic glutamate receptor activity / response to electrical stimulus / response to organonitrogen compound / cellular response to growth factor stimulus / long-term synaptic potentiation / ionotropic glutamate receptor signaling pathway / cellular response to amino acid stimulus / cell adhesion molecule binding / cellular response to manganese ion / hippocampal mossy fiber to CA3 synapse / positive regulation of cell death / response to toxic substance / cerebral cortex development / response to cytokine / hippocampus development / integral component of presynaptic membrane / response to mechanical stimulus / regulation of long-term neuronal synaptic plasticity / memory / presynaptic membrane / terminal bouton / Z disc
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.96 Å resolution
AuthorsKarakas, E. / Furukawa, H.
Funding supportUnited States , 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM105730United States
National Institutes of Health/National Institute of Mental HealthMH085926United States
Robertson Research FundUnited States
Mirus Research AwardUnited States
CitationJournal: Science / Year: 2014
Title: Crystal structure of a heterotetrameric NMDA receptor ion channel.
Authors: Karakas, E. / Furukawa, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 22, 2014 / Release: Jun 4, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 4, 2014Structure modelrepositoryInitial release
1.1Jun 11, 2014Structure modelDatabase references
1.2Jul 30, 2014Structure modelDerived calculations
2.0Sep 6, 2017Structure modelAtomic model / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summaryatom_site / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn / struct_site_gen_atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2B
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,173128
Polyers369,6894
Non-polymers23,484124
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)33250
ΔGint (kcal/M)-717
Surface area (Å2)131720
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)116.825, 163.186, 163.137
Angle α, β, γ (deg.)90.00, 93.81, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules ACBD

#1: Protein/peptide Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 92680.945 Da / Num. of mol.: 2 / Fragment: UNP residues 23-847
Mutation: N61Q, N239D, N350Q, N471Q, N491Q, T561C, E594Q, E595S, E597S, E598T, N771Q, F810C, R844N, R845G, K846A
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35439
#2: Protein/peptide Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B


Mass: 92163.352 Da / Num. of mol.: 2 / Fragment: UNP residues 27-852
Mutation: S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00960

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Non-polymers , 7 types, 124 molecules

#3: Chemical...
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 84 / Formula: W / Tungsten
#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 20 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 5 / Formula: C6H12O6
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 9 / Formula: C6H12O6
#7: Chemical ChemComp-GLY / GLYCINE


Mass: 75.067 Da / Num. of mol.: 2 / Formula: C2H5NO2 / Glycine
#8: Chemical ChemComp-QEL / 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol


Mass: 325.445 Da / Num. of mol.: 2 / Formula: C21H27NO2
#9: Chemical ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 2 / Formula: C5H9NO4 / Glutamic acid

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.2 / Density percent sol: 70.69 %
Crystal growTemp: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG 4000, Tris-HCl, NaCl, Magnesium acetate, metatungstate
PH range: 8.0-8.8

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Collection date: Dec 7, 2013
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 196.24 Å2 / D resolution high: 3.95 Å / D resolution low: 5 Å / Number obs: 52241 / Rmerge I obs: 0.087 / Chi squared: 1.348 / NetI over av sigmaI: 13.025 / NetI over sigmaI: 9.3 / Number measured all: 197482 / Redundancy: 3.8 % / Percent possible obs: 98.6
Reflection shell

Diffraction ID: 1 / Rejects: _

Highest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible allRmerge I obs
3.9504.09052301.1853.70099.400
4.0904.25052601.2653.90099.7000.835
4.2504.45052431.4053.90099.6000.549
4.4504.68052781.4853.90099.6000.383
4.6804.98052511.5193.90099.7000.283
4.9805.36052511.5243.90099.6000.232
5.3605.90052791.4583.90099.7000.189
5.9006.75052771.4463.90099.4000.132
6.7508.50052551.1033.70099.0000.067
8.50050.00049170.9263.10090.9000.050

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3QEL, 2A5T
Overall SU ML: 0.61 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 32.13 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2953 / R factor R work: 0.2563 / R factor obs: 0.2583 / Highest resolution: 3.96 Å / Lowest resolution: 29.717 Å / Number reflection R free: 2625 / Number reflection obs: 52162 / Percent reflection R free: 5.03 / Percent reflection obs: 98.35
Refine hist #finalHighest resolution: 3.96 Å / Lowest resolution: 29.717 Å / B iso mean ligand: 291.34 / Number residues total: 2948
Number of atoms included #finalLigand: 566 / Solvent: 0 / Total: 20246
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220736
X-RAY DIFFRACTIONf_angle_d0.61428679
X-RAY DIFFRACTIONf_dihedral_angle_d10.4136583
X-RAY DIFFRACTIONf_chiral_restr0.0233488
X-RAY DIFFRACTIONf_plane_restr0.0033651
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.960.37090.33654.0343126240091.00
4.03430.36740.32514.11171312621100.00
4.11170.38300.30014.19551492675100.00
4.19550.28210.28914.28641312603100.00
4.28640.31440.26234.38581312630100.00
4.38580.32380.26444.4951158262199.00
4.49510.29620.25714.61631392626100.00
4.61630.27710.24504.7516141260999.00
4.75160.29230.24824.90431302652100.00
4.90430.28660.24615.07871122691100.00
5.07870.30120.25645.28101412629100.00
5.28100.33200.26625.51991512602100.00
5.51990.35360.25885.80891282659100.00
5.80890.31720.26966.1698152262599.00
6.16980.30520.27276.6412135263799.00
6.64120.27240.26437.3006138265899.00
7.30060.26960.24038.3365157261099.00
8.33650.24940.212010.4272138261197.00
10.42720.30670.271329.7182137237888.00

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